The cyclin dependent kinases (CDKs) play a significant role in controlling cell proliferation. Inhibition of CDK2/Cyclin A in G1/S phase of the cell cycle leads to selective apoptosis of cancer cells. Currently available CDK inhibitors primarily target the ATP binding site which is conserved across the family of 516 protein kinases and targeting this site can lead to cross reactivity, side effects and toxicity. In our current study, we are utilizing an alternative approach to inhibit only cell cycle CDKs by targeting the protein-protein interaction on the Cyclin binding groove (CBG) which is distinct from the ATP binding pocket.  The CBG is a hydrophobic groove found only in cell cycle CDKs (Cyclin A, Cyclin D and Cyclin E) through which cyclins recruit substrates and inhibitory proteins. CBG is recognized by a sequence of amino acids present in CDK substrates and potent and selective inhibition of CDK2 is achieved through the octapeptide, HAKRRLIF.  In this study, the N-terminal tetrapeptide was replaced by benzoic acid derivatives using the REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) strategy. Based on these, a series of fragment ligated inhibitory peptides (FLIPs) capable of retaining the majority of the interactions of the parent peptide's N-terminal region were synthesized. Benzoic acid derived FLIPs substituted with basic groups interacting with Glu224 of cyclin A, were among the potent derivatives in the series with IC50 values of less than 10�M. The small molecule N-caps were designed using the LigandFit docking method in Discovery studio 3.5, FLIPs were synthesized by ligating the N-caps to the peptide sequence by solid phase peptide synthesis and further tested for their potency in a fluorescence polarization competitive binding assay. The REPLACE strategy has been successfully applied for the development of more drug-like and non-ATP competitive CDK2 inhibitors as anti-tumor therapeutics.

Optimization of benzoic acid derived inhibitors of the cyclin groove of CDK2 using the REPLACE strategy

246th National Meeting (2013)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.